Dukka Bahadur

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MOTIVATION Accurate computational prediction of protein functional sites is critical to maximizing the utility of recent high-throughput sequencing efforts. Among the available approaches, position-specific conservation scores remain among the most popular due to their accuracy and ease of computation. Unfortunately, high false positive rates remain a(More)
"Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum(More)
With the advent of experimental technologies like chemical cross-linking, it has become possible to obtain distances between specific residues of a newly sequenced protein. These types of experiments usually are less time consuming than X-ray crystallography or NMR. Consequently, it is highly desired to develop a method that incorporates this distance(More)
Protein threading with profiles in which constraints on distances between residues are given is known to be NP-hard. Moreover, a simple algorithm known as CLIQUETHREAD based on efficient reduction to maximum edge-weight clique finding problem has been known to be a practical algorithm for solving the protein threading problem with profiles and constraints.(More)
In nonlinear and chaotic time series prediction, constructing the mathematical model of the system dynamics is not an easy task. Partially connected Artificial Neural Network with Evolvable Topology (PANNET) is a new paradigm for prediction of chaotic time series without access to the dynamics and essential memory depth of the system. Evolvable topology of(More)
The protein threading problem with profiles is known to be efficiently solvable using dynamic programming. In this paper, we consider a variant of the protein threading problem with profiles in which constraints on distances between residues are given. We prove that protein threading with profiles and constraints is NP-hard. Moreover, we show a strong(More)
Prediction of protein functional sites from sequence-derived data remains an open bioinformatics problem. We have developed a phylogenetic motif (PM) functional site prediction approach that identifies functional sites from alignment fragments that parallel the evolutionary patterns of the family. In our approach, PMs are identified by comparing tree(More)
The protein side-chain packing problem is computationally known to be NP-complete [1]. A number of approaches has been proposed for side-chain packing. As the size of the protein becomes larger, the sampling space increases exponentially. Hence, large scale protein side-chain packing In this regard, we had also presented a maximum edge-weight clique based(More)
We have developed a novel approach to solve the protein side-chain packing problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique. Since our approach is based on deterministic algorithms in contrast(More)
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